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Chen C, Zhang X, Li Y, Zou B, Xiao H, Han Y, Yang X, Wu D, Sha L, Yang C, Liu S, Cheng Y, Wang Y, Kang H, Fan X, Zhou Y, Zhang P, Chen ZH, Zhang T, Zhang H. Chromosome-specific painting reveals the Y genome origin and chromosome rearrangements of the St genome in Triticeae. PLANT PHYSIOLOGY 2024; 196:870-882. [PMID: 39158082 DOI: 10.1093/plphys/kiae433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024]
Abstract
Karyotypes provide key cytogenetic information on phylogenetic relationships and evolutionary origins in related plant species. The St genome of Pseudoroegneria contributes to 8 alloploid genera, representing over half of the species that are highly valuable for wheat (Triticum aestivum) breeding and for understanding Triticeae species evolution. However, St chromosome characterization is challenging due to limited cytogenetic markers and DNA information. We developed a complete set of St genome-specific chromosome painting probes for identification of the individual chromosomes 1St to 7St based on the genome sequences of Pseudoroegneria libanotica and wheat. We revealed the conservation of St chromosomes in St-containing species by chromosome painting, including Pseudoroegneria, Roegneria, Elymus, and Campeiostachys. Notably, the Y genome showed hybridization signals, albeit weaker than those of the St genome. The awnless species harboring the Y genome exhibited more intense hybridization signals compare to the awned species in Roegneria and Campeiostachys, yet weaker than the hybridization signals of the St genome in autotetraploid Pseudoroegneria strigosa. Although awnless species were morphologically more similar to each other, phenotypic divergence progressively increased from awnless to awned species. Our results indicate that the Y genome originated from the St genome and shed light on the possible origin of the Roegneria and Campeiostachys species, enhancing our understanding of St-genome-containing species evolution.
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Affiliation(s)
- Chen Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW 2570, Australia
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Xuan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yuling Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Bingcan Zou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - He Xiao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Xunzhe Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Cairong Yang
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130, Sichuan, China
| | - Songqing Liu
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130, Sichuan, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW 2570, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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Dai Y, Fei W, Chen S, Shi J, Ma H, Li H, Li J, Wang Y, Gao Y, Zhu J, Wang B, Chen J, Ma H. Using Transcriptomics to Determine the Mechanism for the Resistance to Fusarium Head Blight of a Wheat- Th. elongatum Translocation Line. Int J Mol Sci 2024; 25:9452. [PMID: 39273397 PMCID: PMC11395471 DOI: 10.3390/ijms25179452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
Fusarium head blight (FHB), caused by the Fusarium graminearum species complex, is a destructive disease in wheat worldwide. The lack of FHB-resistant germplasm is a barrier in wheat breeding for resistance to FHB. Thinopyrum elongatum is an important relative that has been successfully used for the genetic improvement of wheat. In this study, a translocation line, YNM158, with the YM158 genetic background carrying a fragment of diploid Th. elongatum 7EL chromosome created using 60Co-γ radiation, showed high resistance to FHB under both field and greenhouse conditions. Transcriptome analysis confirmed that the horizontal transfer gene, encoding glutathione S-transferase (GST), is an important contributor to FHB resistance in the pathogen infection stage, whereas the 7EL chromosome fragment carries other genes regulated by F. graminearum during the colonization stage. Introgression of the 7EL fragment affected the expression of wheat genes that were enriched in resistance pathways, including the phosphatidylinositol signaling system, protein processing in the endoplasmic reticulum, plant-pathogen interaction, and the mitogen-activated protein kinase (MAPK) signaling pathway at different stages after F. graminearium infection. This study provides a novel germplasm for wheat resistance to FHB and new insights into the molecular mechanisms of wheat resistance to FHB.
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Affiliation(s)
- Yi Dai
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenlin Fei
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Shiqiang Chen
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Juntao Shi
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Haigang Ma
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Haifeng Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jinfeng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yonggang Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yujiao Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jinghuan Zhu
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Bingkui Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianmin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Hongxiang Ma
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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Zhai X, Wu D, Chen C, Yang X, Cheng S, Sha L, Deng S, Cheng Y, Fan X, Kang H, Wang Y, Liu D, Zhou Y, Zhang H. A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance. BMC Genomics 2024; 25:253. [PMID: 38448864 PMCID: PMC10916072 DOI: 10.1186/s12864-024-10140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance. RESULTS In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified. CONCLUSIONS We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.
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Affiliation(s)
- Xingguang Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chen Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaobo Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shuhan Deng
- Glbizzia Biosciences Co., Ltd, Liandong U Valley, Huatuo Road 50, Daxing, Beijing, 102600, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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